ITKWriter can write nrrd files

[dyollb]

Looking through some code I stumbled across this write_seg_nrrd function.

MONAILabel/monailabel/transform/writer.py

Line 69 in 91c48c4

def write_seg_nrrd(

ITK has support for nrrd (reading/writing), so this code could probably use SaveImaged(writer="ITKWriter", ... instead

[jlvahldiek]

ITKWriter supports nrrd, that's correct. As far as I remember, at the time when we committed the write_seg_nrrd function, it was not possible to write multi-channel arrays with overlapping segments using ITKWriter. Is it now possible, @dyollb? @markus-hinsche, maybe you could also add a comment?

[dyollb]

I think so, but I can imagine there may be differences in how the image is written (3D vs 4D) and then interpreted by 3rd party libraries/tools.

For instance, when I write the "probability" channels before doing argmax using SaveImaged, I get two different behaviors

• ITKWriter: writes an image that is interpreted as 3D with N channels by e.g. SimpleITK
• NibabelWriter: is interpreted as 4D by SimpleITK

Btw. I don't think the fact that segments are overlapping should be a problem with ITK, but obviously they need to be stored in separate channels.

[jlvahldiek]

Our intension was to create .seg.nrrd files that are very similar to the ones 3D Slicer creates in order to easily open and visualize these .seg.nrrds in 3D Slicer.
At the time of the commit we did not find a way to get this solved with ITKWriter. Please see also discussion at #779 .

[pieper]

You may want to look into [the SlicerIO[(https://pypi.org/project/slicerio/0.1.5/) package.